Presentation on theme: "Center for Vector Biology"— Presentation transcript:
1Center for Vector Biology Catch the Fever!Calculation of Minimum Field Infection Rates (MFIR) and Maximum Likelihood Estimate (MLE)Lisa Reed, Ph.DCenter for Vector BiologyRutgers University21 April 2011
2What is in this talk? What is an MFIR? History How do we calculate MFIR?Getting data from ESRIFormulas and Pivot Table in ExcelCalculating MFIRWhat is MLEUsing Excel add-in to calculate MLEsDemosWhich is best?AP photo
3Minimum Field Infection Rate Female mosquitoes are live-collected from traps, and grouped by species into vialsEach vial may contain up to a certain number of mosquitoes50 or 75100Pools are evaluated for virus (RT-PCR) and given a positive or negative result.Positive pools are counted, divided by all mosquitoes making up all pools evaluated and multiplied by 1000Total number of positive poolsTotal Number of mosquitoes (positive and negative pools)*1000
4Number of infected mosquitoes per 1000 It represents the MINIMUM numberEach pool acts like a single infected mosquitoA pool can have 30 out of 50 infected but will still only contribute 1 to the rate=66.67=66.67=166.67=33.34
5MFIR History First mention in Proceedings of MFIR values came in 1974 Complicated process to determine arbovirus presenceGrown in cultureCell culture (Vero)Plaque AssayBaby mice, chicks or hamstersTested using hemagglutination, fluorescent antibodyNot computerizedOur understanding of the epidemiology of EEE and other arboviruses were becoming known.
6Getting Your Data Download data from Department of Health site. Use the correct variablesPut the data in the correct formUsing formulas in ExcelUse pivot tables in ExcelApply the formula for MFIR
7Getting Data from the Health Department Go to and log in.Click on “West Nile Virus Surveillance”Go To Mosquito>Reports and Maps>Extract Mosquito Data
9Picking Columns is Critical Lots of columns to choose.Choosing ALL of them can create a HUGE and possibly incomplete data file.There are certain columns you need for calculating infection rates (16):“First 6”USI, SUBUSI, PHELMPID, DATECOLL, SPECIES, MOSCOUNTRESULT, SITENAME, SURVTYPE, LAT, LON, COUNTY, FINSTAT, EEEFINAL, LABNAME, PATHOGEN
14Format/Calculate Variables Formulas:A formula in Excel starts with = or + signA formula in Excel refers to another variable (generally)Week Number formula:+weeknum(date)Pull on bottom cornerto fill column with formula(double click)Substitute Aedes forOchlerotatus
15Preserving Your Changes Copy the column with the formula (highlight and right-mouse click)Paste as “Values”Hit Save
16Using Pivot Tables to Get the Information You Want Pivot Tables Sorts and Manipulates Data in a Summary FashionUses a Layout Wizard to Make Your Choices Easier
17Pivot Table 1Highlight Data (hold down shift key and arrow down, then arrow across)INSERT Pivot Table
18Pivot 2 A new sheet is created Can be modified Lists variables in your datasetHas place for column, row, value and filterWhat do these mean?
19Drag Variables to Label, Value and Filters Drag Species to Row Labels and it will place the species names, one to each rowDrag Results to Column LabelDrag Pathogen to FilterDrag Moscount to Values
20Drag Moscount to Values twice We need both the total number (sums) of mosquitoes tested AND number of pools (counts)Change the values by clicking on moscount down arrow to change value to sums
22Copy Pivot Table to New Sheet Use “Paste Special”Use Values
23Get Rid of Unnecessary Columns Click on column header and control key to select columnsDelete
24Calculate MFIR Add formula to adjacent column (Pos pools)/(Total Mosquitoes) * 1000Fill in formula to end, format if you wish
25Your MFIR valuesYou can add different variables (such as type of trap, months, township) if you are interested in more precise informationYou can use data from different time periodsYou can use this data to justify your actionsDEMO
26MLE History Maximum Likelihood Estimate Statistical term that takes into account POOL SIZENot easy to hand calculateDownload Excel add-in from CDC:Calculates MLE, an adjusted MLE, MFIR and confidence intervals relevant to MLE.MLEs are more accurate when the infection rate is higher or when pool size is large because there is more of a likelihood that a pool will have more than one infected mosquito.